Rising atmospheric CO₂ concentrations and the potential effects of climate change have driven a need to understand the potential of agricultural soils to store carbon (C). In Midwestern cropping systems, alfalfa (Medicago sativa) has received attention from researchers because including it in crop rotations may reduce the net C cost of corn (Zea mays) production. Alfalfa produces large amounts of above- and below-ground biomass that may affect C storage and help build soil carbon over short timeframes. This study investigated how the incorporation of alfalfa regrowth prior to corn affected the soil organic carbon (SOC) and particulate organic matter C (POM-C) pools at two sites in southern Minnesota. The size of the POM C fraction was compared between regrowth treatments after one growing season and δ¹³C stable isotope analysis was used to estimate the relative contributions of corn and alfalfa to POM-C. Changes in δ¹³C in both SOC and POM C were used to determine if the incorporation of alfalfa regrowth increased the contribution of alfalfa to POM-C. Incorporation of alfalfa aboveground biomass stimulated net C mineralization. Incorporated regrowth drove decomposition effects that differentially partitioned biomass inputs between POM-C, SOC, and mineralization. Incorporation of alfalfa standing aboveground biomass may stimulate net soil C decomposition; more research is necessary to determine the factors that influence changes in soil POM-C over longer time frames.